Microbes are the invisible inhabitants of Earth. Yet despite their small size, these organisms can have significant impacts on their environment, including their animal and human hosts. For instance, we now know that specific microbes are important for human health, and are passed from mother to child at birth. Several human diseases have shown a different community of microbes between healthy and sick people.

Eric Hayden, an assistant professor in the Department of Biological Sciences, hopes to add to the rapidly growing field of metagenomics – the modern analysis of complex populations of diverse microorganisms. This approach side-steps the need to grow microbes separately in the lab, and instead studies their DNA taken directly from the environment. Hayden is the recipient of a two-year, $130,772 grant administered by the National Science Foundation’s Established Program to Stimulate Competitive Research (EPSCoR) program.

The grant is designed to allow Hayden to broaden his research interests, and bring back new research capacity to Boise State University and the state of Idaho. Hayden’s past research has been focused on the evolution of RNA molecules, which carry out numerous functions within cells. In particular, he is interested in understanding how new functions – termed “innovations” – emerge through genetic mutation, selection for survival and environmental shifts.

“We create large synthetic libraries of genetic variants and determine how good each one is at it’s job, which we call ‘RNA fitness’. Then, we try to understand how fitness changes as the genetic sequence changes,” Hayden said. “Ultimately, we’re trying to predict or forecast evolutionary outcomes.”

The EPSCoR grant will allow Hayden to scale his research up from populations of molecules to populations of microbes. The project will be in collaboration with biological sciences associate professor Jen Forbey, who is trying to understand why some animals can eat sagebrush – a plant that is toxic to most animals.

“Sagebrush is defended chemically and most things avoid it,” Hayden said. “But there are a few specific critters that have herbivore specialization – like koalas eating eucalyptus. We think a lot of this specialization happens microbially, in their guts.”

The research will aim to identify differences in the communities of microbes in specific herbivores over time and as they eat different food sources. The duo is hoping to find correlation between specific types of bacteria and specific animal diets. They also want to identify functions and mechanisms through the discovery of new genes and new gene regulatory elements. In short, they plan to discover how the microbes deal with these plant-derived chemicals, which may lead to new ways to chemically synthesize plant molecules, discover new antimicrobial drugs or combat animals and insects that eat commercially and ecologically important plants.

Hayden will work with the laboratory of Rob Knight at the University of California at San Diego, a leader in metagenomics research. Hayden plans to advance his skills required for this research, and to pass these skills on to students and other researchers across the state. In addition, the computational analysis of DNA sequence data, or bioinformatics, also is required for his current research on RNA. He will advance these efforts as well.

“It’s really exciting to go to where this cutting-edge research is happening, where they’re developing the computational tools to analyze the data, which is an area where we need to advance our skills at Boise State,” Hayden said. “The data analyst skills needed to do this research are the same skills needed in many sectors of the economy. This means that students trained in this type of biological research will have many doors open for them, even outside of biological research.”

EPSCoR provides 30 non-tenured researchers annually with fellowships that put them in partnership with premier research centers, enhancing their ability to work at the frontiers of science and engineering. Two awards were granted to Boise State researchers this year, one to Hayden and another to Lisa Warner from the Department of Chemistry and Biomolecular Research Center.